#!/usr/bin/perl -w

use strict;

my @unordered = qw( 
  2HB 3HB C CA CB CG CD1 
  CD2 CE1 CZ CE2 HE2 HE1
  HH HD1 HD2 N O OH
);

# weighting hashes
my %main = (
  N => '1',
  CA => '2',
  C => '3',
  O => '4', 
  S => '5',
  P => '6',
  H => '7',
);

my %greek = (
  B => '1',
  G => '2',
  D => '3',
  E => '4',
  Z => '5',
  H => '6', 
);

sub sortable {
  my $atom = shift;

  # get components
  $atom =~ /(\d)?(N|CA|C|O|S|P|H)(B|G|D|E|Z|H)?(\d)?/;
  my ($left,$main,$greek,$right) = ( $1, $2, $3, $4 );

  # get weights or use default early sorting values
  $main = $main ? $main{ $main } : '0';
  my $main_alone; # need to flag if main element is alone
  if ( $greek ) {
    $main_alone = '1';
    $greek = $greek{ $greek };
  } else {
    $main_alone = '0';
    $greek = '0';
  } 
  $left  ||= '0';
  $right ||= '0';

  # I assume that left numbers take precedence over right
  "$main_alone$main$greek$left$right";   
}

# use the string "cmp" operator - we are comparing strings,
# not numbers. We could have populated
# the weighting hashes with letters instead of numbers

my @ordered = sort { sortable( $a ) cmp sortable( $b ) } @unordered;

# if you have to get the value out of an object it would be:
# @ordered = sort { sortable( $a->AtomName ) cmp sortable( $b->AtomName ) } @unordered;

print join "\n", map { $_ ."\t". sortable( $_ ) } @ordered;